During the late Neogene, the Lambert Glacier–Amery Ice Shelf drainage system flowed across Prydz Bay and showed several changes in flow pattern. In the Early Pliocene, the Lambert Glacier ice stream reached the shelf edge and built a trough mouth fan on the upper continental slope. This was associated with an increase in ice discharge from the Princess Elizabeth Land coast into Prydz Bay. The trough mouth fan consists mostly of debris flow deposits derived from the melting out of subglacial debris at the grounding line at the continental shelf edge. The composition of debris changes at around 1.1 Ma BP from material derived from erosion of the Lambert Graben and Prydz Bay Basin to mostly basement derived material. This probably results from a reduction in the depth of erosion and hence the volume of ice in the system. In the trough mouth fan, debris flow intervals are separated by thin mudstone horizons deposited when the ice had retreated from the shelf edge. Age control in an Ocean Drilling Program hole indicates that most of the trough mouth fan was deposited prior to the Brunhes–Matuyama Boundary (780 ka BP). This stratigraphy indicates that extreme ice advances in Prydz Bay were rare after the mid Pleistocene, and that ice discharge from Princess Elizabeth Land became more dominant than the Lambert Glacier ice in shelf grounding episodes, since the mid Pleistocene. Mechanisms that might have produced this change are extreme inner shelf erosion and/or decreasing ice accumulation in the interior of East Antarctica. We interpret this pattern as reflecting the increasing elevation of coastal ice through time and the increasing continentality of the interior of the East Antarctic Ice Sheet. The mid Pleistocene change to 100 ka climatic and sea level cycles may also have affected the critical relationship between ice dynamics and the symmetry or asymmetry of the interglacial/glacial climate cycle duration.